S2s prototype4

README.md

@@ -86,6 +86,13 @@ module load rocoto
 rocotorun -w workflow.xml -d workflow.db
 ```
 
+## Using crons on Orion 
+
+On orion, you will need to update the path to rocotorun in the autogenerated workflow.crontab  to be
+/apps/contrib/rocoto/1.3.1/bin/rocotorun
+
+Also note, on orion you need to be on login node 1 for cronjobs. 
+
 ## Resource handling
 There are two ways of changing resource settings (cpu count, time limits, threads) for a job that has already been defined in the workflow.
 

env/ORION.env

@@ -42,20 +42,11 @@ if [ $step = "prep" -o $step = "prepbufr" ]; then
     export BACK=${BACK:-"YES"}
     export sys_tp="ORION"
 
-elif [ $step = "waveinit" -o $step = "waveprep" ]; then
-
-    export mpmd="--multi-prog"
-    export CFP_MP="YES"
-
 elif [ $step = "anal" ]; then
 
     export MKL_NUM_THREADS=4
     export MKL_CBWR=AUTO
 
-    export USE_CFP=${USE_CFP:-"YES"}
-    export CFP_MP="YES"	# For analdiag with SLURM
-    export APRUNCFP="$launcher"
-
     nth_max=$(($npe_node_max / $npe_node_anal))
 
     export NTHREADS_GSI=${nth_anal:-$nth_max}

jobs/JGLOBAL_FORECAST

@@ -9,7 +9,7 @@ date
 #############################
 # Source relevant config files
 #############################
-configs="base fcst"
+configs="base fcst wave"
 export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
 config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
 for config in $configs; do

jobs/JWAVE_POST_SBS

@@ -7,7 +7,7 @@ set -x -e
 #############################
 # Source relevant config files
 #############################
-configs="base wave wavepostsbs"
+configs="base wave"
 export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
 config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
 for config in $configs; do
@@ -36,6 +36,9 @@ export DATA=${DATA:-${DATAROOT}/${jobid:?}}
 mkdir -p $DATA
 cd $DATA
 
+cyc=${cyc:-00}
+export cycle=${cycle:-t${cyc}z}
+
 # Set PDY
 setpdy.sh
 sh ./PDY

jobs/JWAVE_PREP

@@ -50,9 +50,9 @@ export RPDY=$PDY
 
 export pgmout=OUTPUT.$$
 
-export COMINice=$((COMINice:-$COMROOTp2/omb/prod))
-export COMINwnd=$((COMINwnd:-$COMROOT/gfs/prod))
-export COMIN_WAV_CUR=$((COMIN_WAV_CUR:-$COMROOTp2/rtofs/prod))
+export COMINice=${COMINice:-${COMROOTp2}/omb/prod}
+export COMINwnd=${COMINwnd:-${COMROOT}/gfs/prod}
+export COMIN_WAV_CUR=${COMIN_WAV_CUR:-${COMROOTp2}/rtofs/prod}
 
 export COMINwave=${COMINwave:-${ROTDIR:?}}
 export COMOUTwave=${COMOUTwave:-${ROTDIR:?}}

modulefiles/module-setup.sh.inc

@@ -31,7 +31,7 @@ elif [[ -d /scratch1 ]] ; then
 elif [[ -d /work ]] ; then
     # We are on MSU Orion
     if ( ! eval module help > /dev/null 2>&1 ) ; then
-        source /apps/lmod/init/$__ms_shell
+        source /apps/lmod/lmod/init/$__ms_shell
     fi
     module purge
 elif [[ -d /gpfs/hps && -e /etc/SuSE-release ]] ; then

modulefiles/module_base.orion

@@ -6,28 +6,37 @@
 ## load contrib environment
 ## load slurm utils (arbitrary.pl  layout.pl)
 ##
+module load contrib noaatools
+
 ##
 ## load programming environment
 ## this typically includes compiler, MPI and job scheduler
 ##
-module load intel/2018.4
-module load impi/2018.4
-module load wgrib/2.0.8
-module load nco/4.8.1
+module load intel/2018
+module load impi/2018
 
-module load gempak/7.5.1
+#For ocean post: 
+module load ncl/6.6.2
+module load nco/4.8.1
 
 ##
 ## NCEP libraries (temporary version to match the CCPP requirements)
 ##
 module use /apps/contrib/NCEPLIBS/orion/modulefiles
-module load grib_util/1.2.0
-module load prod_util/1.2.0
+module load bacio/2.0.3
+module load ip/3.0.2
+module load nemsio/2.2.4
+module load sp/2.0.3
+module load w3emc/2.4.0
+module load w3nco/2.0.7
+module load g2/3.1.1
 module load g2tmpl/1.6.0
 module load crtm/2.3.0
-module load netcdf_parallel/4.7.4
-module load hdf5_parallel/1.10.6
+module load jasper/1.900.2
+module load png/1.2.44
+module load z/1.2.6
 
+module load prod_util/1.2.0
 ##
 ## load ESMF library for above compiler / MPI combination
 ## use pre-compiled EMSF library for above compiler / MPI combination
@@ -37,13 +46,16 @@ module load netcdfp/4.7.4
 module load esmflocal/8.0.0.para
 module load post-intel-sandybridge/8.0.5
 
-module load contrib
-module load rocoto/1.3.1
-module load slurm/19.05.3-2
 
-# Python
-module load python/3.7.5
+module load netcdf_parallel/4.7.4
+module load hdf5_parallel/1.10.6
+module load wgrib/2.0.8
+module load grib_util/1.2.0
+
+module load slurm/19.05.3-2
 
+##
+### load cmake
 ###
 module load cmake/3.15.4
 setenv CMAKE_C_COMPILER mpiicc

scripts/exwave_prep.sh

@@ -30,7 +30,6 @@
 # Nov2012 JHAlves - Transitioning to WCOSS                                    #
 # Apr2019 JHAlves - Transitioning to GEFS workflow                            #
 # Nov2019 JHAlves - Merging wave scripts to global workflow                   #
-# Jun2020 JHAlves - Porting to R&D machine Hera                               #
 #                                                                             #
 #   WAV_MOD_ID and WAV_MOD_TAG replace modID. WAV_MOD_TAG                     # 
 #   is used for ensemble-specific I/O. For deterministic                      #

sorc/build_fv3_coupled.sh

@@ -16,7 +16,6 @@ if [ ! -d "../exec" ]; then
   mkdir ../exec
 fi
 
-if [ $target = theia ]; then target=theia.intel ; fi
 
 cd fv3_coupled.fd/NEMS 
 make -j 8 app=coupledFV3_CCPP_MOM6_CICE_WW3 build

sorc/checkout.sh

@@ -16,7 +16,7 @@ rm -f ${topdir}/checkout-fv3_coupled.log
 if [[ ! -d fv3_coupled.fd ]] ; then
     git clone https://github.com/ufs-community/ufs-s2s-model fv3_coupled.fd >> ${topdir}/checkout-fv3_coupled.log 2>&1
     cd fv3_coupled.fd
-    git checkout s2s_prototype4.0
+    git checkout ufss2s_cmeps_v0.7 
     git submodule update --init --recursive
     cd ${topdir}
 else

sorc/link_fv3gfs.sh

@@ -344,7 +344,7 @@ cd $pwd/../parm/config
 #fi
 #------------------------------
 if [ $model = "coupled" ] ; then
- rm -f config.base
+ #rm -f config.base
  #cp -p config.base.emc.dyn_coupled config.base
  cd $pwd/../fix
  # Add fixed files needed for coupled ufs-s2s-model